Variant report

Variant	rs17728678
Chromosome Location	chr8:11116661-11116662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11111015..11113858-chr8:11114874..11117999,4	K562	blood:

Variant related genes	Relation type
ENSG00000239315	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10503419	0.82[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11250125	1.00[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11986879	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11990279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11990306	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11992965	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11994225	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11996245	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11996437	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11997943	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17728696	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17796046	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17796070	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2082775	0.91[GIH][hapmap];0.81[EUR][1000 genomes]
rs56071200	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56246833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73198998	0.86[EUR][1000 genomes]
rs73205327	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73205329	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73205330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73205332	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73205333	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73205334	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73205336	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73205339	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73205340	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73205341	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs956669	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17728678	DEFB136	cis	parietal	SCAN
rs17728678	CTSB	cis	cerebellum	SCAN
rs17728678	FLJ10661	cis	cerebellum	SCAN
rs17728678	FAM167A	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11116000-11116800	Enhancers	H1 Cell Line	embryonic stem cell
2	chr8:11116000-11116800	Enhancers	H9 Cell Line	embryonic stem cell
3	chr8:11116000-11116800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr8:11116000-11116800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr8:11116000-11117200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr8:11116200-11116800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:11116200-11116800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr8:11116200-11116800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr8:11116200-11117200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr8:11116400-11119000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr8:11116600-11117200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr8:11116600-11118400	Weak transcription	Colon Smooth Muscle	Colon
13	chr8:11116600-11119200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr8:11116600-11119200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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